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C4-like Sesuvium sesuvioides (Aizoaceae) exhibits CAM in cotyledons and putative C4-like + CAM metabolism in adult leaves as revealed by transcriptome analysis
BackgroundThe co-occurrence of C 4 and CAM photosynthesis in a single species seems to be unusual and rare. This is likely due to the difficulty in...
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Unveiling the translational dynamics of lychee (Litchi chinesis Sonn.) in response to cold stress
Cold stress poses a significant threat to the quality and productivity of lychee ( Litchi chinensis Sonn . ). While previous research has extensively...
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A systematic strategy for identifying causal single nucleotide polymorphisms and their target genes on Juvenile arthritis risk haplotypes
BackgroundAlthough genome-wide association studies (GWAS) have identified multiple regions conferring genetic risk for juvenile idiopathic arthritis...
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METASEED: a novel approach to full-length 16S rRNA gene reconstruction from short read data
BackgroundWith the emergence of Oxford Nanopore technology, now the on-site sequencing of 16S rRNA from environments is available. Due to the error...
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expHRD: an individualized, transcriptome-based prediction model for homologous recombination deficiency assessment in cancer
BackgroundHomologous recombination deficiency (HRD) stands as a clinical indicator for discerning responsive outcomes to platinum-based chemotherapy...
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Comprehensive analysis of the Xya riparia genome uncovers the dominance of DNA transposons, LTR/Gypsy elements, and their evolutionary dynamics
Transposable elements (TEs) are DNA sequences that can move or replicate within a genome, and their study has become increasingly important in...
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A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques
BackgroundThe growing abundance of in vitro omics data, coupled with the necessity to reduce animal testing in the safety assessment of chemical...
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Expression genome-wide association study identifies key regulatory variants enriched with metabolic and immune functions in four porcine tissues
BackgroundIntegration of high throughput DNA genoty** and RNA-sequencing data enables the discovery of genomic regions that regulate gene...
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SimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies
BackgroundSimSpliceEvol is a tool for simulating the evolution of eukaryotic gene sequences that integrates exon-intron structure evolution as well...
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OBSERVE: guidelines for the refinement of rodent cancer models
Existing guidelines on the preparation (Planning Research and Experimental Procedures on Animals: Recommendations for Excellence (PREPARE)) and...
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Genome-wide analysis of histone modifications can contribute to the identification of candidate cis-regulatory regions in the threespine stickleback fish
BackgroundCis -regulatory mutations often underlie phenotypic evolution. However, because identifying the locations of promoters and enhancers in...
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Comparative proteomics in tall fescue to reveal underlying mechanisms for improving Photosystem II thermotolerance during heat stress memory
BackgroundThe escalating impacts of global warming intensify the detrimental effects of heat stress on crop growth and yield. Among the earliest and...
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Mendelian randomization analysis reveals higher whole body water mass may increase risk of bacterial infections
Background and purposeThe association of water loading with several infections remains unclear. Observational studies are hard to investigate...
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Association between OX40L polymorphism and type 2 diabetes mellitus in Iranians
IntroductionDiabetes mellitus (DM) is one of the leading causes of morbidity and mortality worldwide. It is a multifactorial disease that genetic and...
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Understanding the responses of tillering to 2,4-D isooctyl ester in Setaria viridis L.
BackgroundGreen foxtail [ Setaria viridis (L.)] is one of the most abundant and troublesome annual grass weeds in alfalfa fields in Northeast China....
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Population structure and selection signal analysis of indigenous sheep from the southern edge of the Taklamakan Desert
Analyzing the genetic diversity and selection characteristics of sheep (Ovis aries) holds significant value in understanding their environmental...
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gcplyr: an R package for microbial growth curve data analysis
BackgroundCharacterization of microbial growth is of both fundamental and applied interest. Modern platforms can automate collection of...
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ProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing
BackgroundStructural variations play an important role in bacterial genomes. They can mediate genome adaptation quickly in response to the external...
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Rapid evolution of promoters from germline-specifically expressed genes including transposon silencing factors
BackgroundThe piRNA pathway in animal gonads functions as an ‘RNA-based immune system’, serving to silence transposable elements and prevent...
